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Search: Posts Made By: fjrossello
Forum: Bioinformatics 07-07-2014, 04:07 PM
Replies: 1
Views: 1,114
Posted By fjrossello
Hi Guys, For all those experiencing this...

Hi Guys,

For all those experiencing this issue, find the discussion and solution here (https://www.biostars.org/p/105296/#105720).

Cheers,

Fernando
Forum: Bioinformatics 06-30-2014, 07:45 PM
Replies: 1
Views: 1,114
Posted By fjrossello
Breakdancer inaccurate output.

Hi Guys,

I have run Breakdancer on a mouse KO sample and got several lines containing intrachromosomal translocations but described as interchromosomal, i. e., CTX instead of ITX, according to...
Forum: General 01-28-2013, 02:16 PM
Replies: 23
Views: 111,196
Posted By fjrossello
Excellent Jamie. Thanks. I will cite the...

Excellent Jamie. Thanks. I will cite the SEQanswers paper and attach the URL if I use information from the forum.

Cheers,

Fernando
Forum: Bioinformatics 01-27-2013, 01:54 PM
Replies: 6
Views: 1,130
Posted By fjrossello
I agree with Dietmar13. In the Circos webpage you...

I agree with Dietmar13. In the Circos webpage you can find examples that are/were used for Genomics. In gral., people use scatter or line plots for CNVs, the classical links for inter and...
Forum: General 01-27-2013, 01:49 PM
Replies: 23
Views: 111,196
Posted By fjrossello
Thanks. I will do as suggested. Cheers, ...

Thanks. I will do as suggested.
Cheers,
Fernando
Forum: General 01-27-2013, 04:12 AM
Replies: 23
Views: 111,196
Posted By fjrossello
Hi All, My apologies if this is not the...

Hi All,

My apologies if this is not the right place to place this question but I am curious about this issue.
I started a thread on acknowledging posts on the site -...
Forum: General 01-22-2013, 05:23 AM
Replies: 0
Views: 6,437
Posted By fjrossello
Acknowledge/Cite Seqanswers posts and/or community.

Hi all,

I was wondering if anyone could explain or clarify for me how should I acknowledge or, if possible, cite an specific post within Seqanswers. I am aware that there's been a recent...
Forum: Literature Watch 01-21-2013, 02:36 PM
Replies: 76
Views: 30,656
Posted By fjrossello
Hi Valeu, Sorry to be so insistent in this...

Hi Valeu,

Sorry to be so insistent in this aspect. I re-run control-freec on an mpileup file of one my samples with and without BAF options and I found a few differences between both runs. First,...
Forum: Literature Watch 01-18-2013, 02:00 PM
Replies: 76
Views: 30,656
Posted By fjrossello
Thanks for your prompt answer. I understand. I...

Thanks for your prompt answer. I understand. I will anxiously wait for the next version, speed improvements and bug corrections are always good news.
Just to be clear, when you use a pileup file,...
Forum: Literature Watch 01-17-2013, 06:44 PM
Replies: 76
Views: 30,656
Posted By fjrossello
Hi Valeu, This is Fernando again. I have...

Hi Valeu,

This is Fernando again. I have re-run Freec on one of my samples where I previously run CNA analysis from a SAM file (unsorted, I use the FR mateOrientation parameter). The difference ...
Forum: Literature Watch 12-21-2012, 03:05 PM
Replies: 76
Views: 30,656
Posted By fjrossello
Hi Valeu, Thanks for your explanation and in...

Hi Valeu,
Thanks for your explanation and in regards to the R plots, I downloaded the latest makeGraph.R and works perfectly.
Cheers,
Fernando
Forum: Literature Watch 12-20-2012, 01:51 PM
Replies: 76
Views: 30,656
Posted By fjrossello
Hi Valeu, I am using control-freec to detect...

Hi Valeu,

I am using control-freec to detect CNV and LOH in normal vs tumor samples (low pass whole genome).
I had no problems to run it at all. However, I would like to ask you a couple of...
Forum: RNA Sequencing 12-07-2012, 03:32 PM
Replies: 2
Views: 1,199
Posted By fjrossello
Hi Stephio, Just a comment. I use a similar...

Hi Stephio,

Just a comment. I use a similar approach - no CleanSam step used - for exome capture analysis and got comparable results. IMHO, the protocol We are currently following is standard and...
Forum: Genomic Resequencing 11-11-2012, 02:31 PM
Replies: 1
Views: 836
Posted By fjrossello
Hi Navik, Perform a QA/QC of your raw reads...

Hi Navik,

Perform a QA/QC of your raw reads first. Then, If a reference genome is available, I would align your raw sequences first using a read aligner such as bwa or bowtie. Bear in mind that...
Forum: Bioinformatics 11-09-2012, 02:26 AM
Replies: 4
Views: 2,786
Posted By fjrossello
Excellent! Thanks. Cheers, Fernando

Excellent! Thanks.
Cheers,
Fernando
Forum: Bioinformatics 11-08-2012, 08:51 PM
Replies: 4
Views: 2,786
Posted By fjrossello
Hi Filip, The same problem here (end to end,...

Hi Filip,

The same problem here (end to end, MapQual all 0s. However, this only happened when --no-mixed --no-discordant options were used. Find the parameters below:

bowtie2 -p 6 --phred33 -N...
Forum: Bioinformatics 11-05-2012, 11:35 PM
Replies: 3
Views: 2,151
Posted By fjrossello
Hi Jane, As you could tell from my previous...

Hi Jane,

As you could tell from my previous post, I had the same issue. I found a putative solution to your problem.
I understand you have aligned your files using novoalign and I do not know if...
Forum: Bioinformatics 11-05-2012, 09:52 PM
Replies: 3
Views: 2,151
Posted By fjrossello
Hi Guys, Same issue with me when running a...

Hi Guys,

Same issue with me when running a bam file resulting from merging 3 different samples.
Any ideas?
Thanks in advance.

Cheers,

Fernando
Forum: Bioinformatics 10-28-2012, 05:59 PM
Replies: 0
Views: 1,517
Posted By fjrossello
Bowtie2 output options

Hi guys,

I have been trying to write unaligned (--un path) and aligned (--al path) reads from a Bowtie2 (Bowtie2 2.0.0-beta7) alignment without success. It is PE 100 bp Illumina exome data. If I...
Forum: Bioinformatics 10-11-2012, 05:48 PM
Replies: 31
Views: 7,370
Posted By fjrossello
[/QUOTE] Hi Tankman, Sorry for my late...

[/QUOTE]

Hi Tankman,

Sorry for my late reply. As previously discussed, find below the output from tophat fusion. It worked and I obtained the same output as before.
Have yo been able to solve...
Forum: Bioinformatics 10-03-2012, 03:56 AM
Replies: 31
Views: 7,370
Posted By fjrossello
Hi Tankman, Q1: Yes, I tested the output of...

Hi Tankman,

Q1: Yes, I tested the output of that test-sample and I then processed my own.
Q2: Yes, I used tophat 2.0.3 for those reads and I am currently using TopHat 2.0.4. Unfortunately, I will...
Forum: Bioinformatics 10-02-2012, 08:46 PM
Replies: 31
Views: 7,370
Posted By fjrossello
Hi Tankman, Find below my directory...

Hi Tankman,

Find below my directory structure:

Total 48K
32K drwxr-xr-x 2 fernandr hpcmimr 16K Jun 22 12:33 blast
0 -rw-r--r-- 1 fernandr hpcmimr 38M Jun 22 12:33 ensGene.txt
0...
Forum: Bioinformatics 08-14-2012, 02:31 AM
Replies: 5
Views: 4,652
Posted By fjrossello
Hi Guys, I got a similar error message in...

Hi Guys,

I got a similar error message in regards to /fix_map_ordering: /usr/lib64/libz.so.1: no version information available . However, TopHat completes the run. As far as I understand, this...
Forum: Bioinformatics 08-07-2012, 04:33 AM
Replies: 5
Views: 7,726
Posted By fjrossello
Excellent Simon. Thanks!

Excellent Simon. Thanks!
Forum: Bioinformatics 07-31-2012, 07:44 PM
Replies: 24
Views: 3,587
Posted By fjrossello
Hi Sarah, Your reads look as if they were...

Hi Sarah,

Your reads look as if they were produced with CASAVA v1.8, which reports Phred+33 Q-scores (Illumina 1.9/Sanger). If that is the case, removing the --phred64-quals option from the bowtie...
Showing results 1 to 25 of 30

 


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